Houghton took over as Chief of the Defence Staff on 18 July 2013.[16] He has stated that one of his key objectives is to re-shape the Armed forces in the post-Afghanistan era.[17] Houghton has also raised concerns about the Armed Forces' abilities with the personnel and budget cuts.[18] As of 2015, Houghton was paid a salary of between £255,000 and £259,999 by the department, making him one of the 328 most highly paid people in the British public sector at that time.[19]

In January 2016, the government announced that Houghton would be replaced by Sir Stuart Peach as Chief of the Defence Staff in the summer of 2016.[20] Houghton handed over to Peach on 14 July 2016.[21]

In October 2017, it was announced that a life peerage would be conferred on Houghton.[40][41] On 20 November, he was created Baron Houghton of Richmond, of Richmond in the County of North Yorkshire.[42]